Casal2 Test Case comparisons for LIN5/6

1 LIN5/6 comparison of CASAL and Casal2 model configurations

This document compares the results of at least 2 CASAL model configurations (base and at least one sensitivity) and up to 8 Casal2 model configurations (3 BetaDiff, 2 CppAD, and 3 ADOL-C).

The CASAL model sensitivity 1 has a smaller tolerance value than the CASAL base model (1e-6 vs. 2e-3).

The Casal2 ADOL-C and BetaDiff low tolerance models have a smaller tolerance value than the CASAL base model (1e-6 vs. 2e-3). The Casal2 CppAD models have a tolerance value of 1e-9.

1.1 LIN5/6 model characteristics

The main characteristics of the Test Case LIN5/6 (ling) CASAL model are:

• one stock, ages 3 - 25
• one area
• years 1972 - 2018, projection years 2019 - 2023
• two time steps: Dec_Aug and Sep_Nov
• two stock categories: male and female
• natural mortality-at-age is double exponential
• sex-specific maturity ogives specified by age
• sex-specific age-length von Bertalanffy relationship
• sex-specific length-weight relationship
• Beverton-Holt stock-recruitment relationship, with steepness (h) set to 0.84
• ageing error
• two surveys with sex-specific logistic selectivity
• three fisheries, one with double normal selectivity and two with logistic selectivity

Observation data include:

• survey indices
• survey proportions-at-age
• fishery proportions-at-age

Parameters estimated include:

• B0
• parameters for the natural mortality-at-age ogive
• free catchability (q) for the two surveys
• parameters for the sex-specific selectivity curves for the two surveys
• parameters for the sex-specific selectivity curves for the three fisheries
• year-class strengths (recruitment deviations)

1.2 R environment

## [1] "Thu May 28 17:13:22 2020"

## R version 3.6.3 (2020-02-29)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Debian GNU/Linux bullseye/sid
## 
## Matrix products: default
## BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
## 
## locale:
##  [1] LC_CTYPE=en_NZ.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_NZ.UTF-8        LC_COLLATE=en_NZ.UTF-8    
##  [5] LC_MONETARY=en_NZ.UTF-8    LC_MESSAGES=en_NZ.UTF-8   
##  [7] LC_PAPER=en_NZ.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_NZ.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] casal2_1.0     casal_2.30     devtools_2.3.0 usethis_1.6.1  rlist_0.4.6.1 
## [6] ggplot2_3.3.0 
## 
## loaded via a namespace (and not attached):
##  [1] Rcpp_1.0.4.6      pillar_1.4.4      compiler_3.6.3    remotes_2.1.1    
##  [5] prettyunits_1.1.1 tools_3.6.3       testthat_2.3.2    pkgload_1.0.2    
##  [9] pkgbuild_1.0.8    digest_0.6.25     memoise_1.1.0     evaluate_0.14    
## [13] lifecycle_0.2.0   tibble_3.0.1      gtable_0.3.0      pkgconfig_2.0.3  
## [17] rlang_0.4.6       cli_2.0.2         yaml_2.2.1        xfun_0.14        
## [21] withr_2.2.0       stringr_1.4.0     dplyr_0.8.5       knitr_1.28       
## [25] desc_1.2.0        vctrs_0.3.0       fs_1.4.1          rprojroot_1.3-2  
## [29] grid_3.6.3        tidyselect_1.1.0  glue_1.4.1        data.table_1.12.8
## [33] R6_2.4.1          processx_3.4.2    fansi_0.4.1       rmarkdown_2.1    
## [37] sessioninfo_1.1.1 callr_3.4.3       purrr_0.3.4       magrittr_1.5     
## [41] backports_1.1.7   ps_1.3.3          scales_1.1.1      ellipsis_0.3.1   
## [45] htmltools_0.4.0   assertthat_0.2.1  colorspace_1.4-1  stringi_1.4.6    
## [49] munsell_0.5.0     crayon_1.3.4

1.3 CASAL and Casal2 model output

# read in CASAL MPD results
cas_mpd_filename <- file.path(base_dir, 'CASAL', mpd_run)
cas_mpd  <- casal::extract.mpd(cas_mpd_filename)
cas_corr <- casal::extract.correlation.matrix(cas_mpd_filename)
cas_conv <- get_convergence_information(cas_mpd_filename)
c1_quant <- cas_mpd$quantities

cas_mpd_sens1_filename <- file.path(base_dir, 'CASAL_sens1', mpd_run)
cas_mpd_sens1  <- casal::extract.mpd(cas_mpd_sens1_filename)
cas_sens1_corr <- casal::extract.correlation.matrix(cas_mpd_sens1_filename)
cas_sens1_conv <- get_convergence_information(cas_mpd_sens1_filename)
c1_sens1_quant <- cas_mpd_sens1$quantities

C2_subdir <- c('betadiff_casal_flags_on',
               'betadiff_casal_flags_off',
               'betadiff_casal_flags_on_low_tol',
               'cppad_casal_flags_on',
               'cppad_casal_flags_off',
               'adolc_casal_flags_on',
               'adolc_casal_flags_off',
               'adolc_casal_flags_on_low_tol')


# find the non-zero-sized parameter estimate files for the C2 models
C2_subdir <- unlist(sapply(C2_subdir, function(c_dir) if ( file.access(file.path(base_dir, 'Casal2', c_dir, params_est), 4) == 0 &
                                                           file.size(file.path(base_dir, 'Casal2', c_dir, params_est)) > 0 )
                                                         { return (c_dir) }, USE.NAMES=FALSE ))


num_C2_models <- length(C2_subdir)

C2_color <- c('blue', 'green3', 'red', 'gold', 'magenta', 'cyan', 'brown', 'orange')

# read in Casal2 MPD results
cas2_mpd  <- list()
cas2_corr <- list()
cas2_conv <- list()
for (c in 1:num_C2_models)
{
    cas2_mpd_filename <- file.path(base_dir, 'Casal2', C2_subdir[c], mpd_run)
    cas2_mpd[[c]] <- casal2::extract.mpd(cas2_mpd_filename)

    cas2_corr[[c]] <- casal2::extract.correlation.matrix(mpd_out, file.path(base_dir, 'Casal2', C2_subdir[c]))

    cas2_conv[[c]] <- get_convergence_information(cas2_mpd_filename)
}

1.4 Tables

Tables of parameter estimates and objective function components for the CASAL and Casal2 model MPD results

CASAL parameter estimates and Percent Difference

rownames	Base_Model	Sensitivity_1	Percent_Diff
q[tan_sum].q	0.09128	0.09105	0.251
q[tan_aut].q	0.12625	0.12592	0.258
initialization.B0	308952.00000	310671.00000	-0.556
natural_mortality.ogive_all1	12.49210	12.98210	-3.922
natural_mortality.ogive_all2	0.13271	0.12782	3.680
natural_mortality.ogive_all3	0.38192	0.44986	-17.790
natural_mortality.ogive_all4	0.35058	0.35395	-0.960
selectivity[surveysum_sel].male1	4.73847	4.88131	-3.014
selectivity[surveysum_sel].male2	1.74997	1.77236	-1.279
selectivity[surveysum_sel].male3	0.61001	0.60162	1.375
selectivity[surveysum_sel].female1	5.46022	5.61310	-2.800
selectivity[surveysum_sel].female2	2.20584	2.21537	-0.432
selectivity[surveyaut_sel].male1	5.50416	5.64383	-2.538
selectivity[surveyaut_sel].male2	2.31427	2.29812	0.698
selectivity[surveyaut_sel].male3	0.93922	0.93314	0.648
selectivity[surveyaut_sel].female1	5.92021	6.06245	-2.403
selectivity[surveyaut_sel].female2	2.77781	2.73777	1.441
selectivity[trawl_sel].male1	8.36987	8.40438	-0.412
selectivity[trawl_sel].male2	1.97182	1.94699	1.259
selectivity[trawl_sel].male3	61.64930	200.00000	-224.416
selectivity[trawl_sel].male4	1.04125	1.02062	1.981
selectivity[trawl_sel].female1	8.66384	8.74135	-0.895
selectivity[trawl_sel].female2	2.09989	2.08792	0.570
selectivity[trawl_sel].female3	43.31110	40.38180	6.763
selectivity[line_home_sel].male1	11.45120	8.58352	25.043
selectivity[line_home_sel].male2	8.59023	4.54774	47.059
selectivity[line_home_sel].male3	0.38005	0.26910	29.193
selectivity[line_home_sel].female1	9.61555	9.53091	0.880
selectivity[line_home_sel].female2	3.87496	3.68517	4.898
selectivity[line_spawn_sel].male1	18.29980	14.03630	23.298
selectivity[line_spawn_sel].male2	13.66550	10.01380	26.722
selectivity[line_spawn_sel].male3	1.86791	1.17322	37.191
selectivity[line_spawn_sel].female1	9.74583	9.71344	0.332
selectivity[line_spawn_sel].female2	3.00787	2.89355	3.801
recruitment.YCS1	1.00000	1.00000	0.000
recruitment.YCS2	1.00000	1.00000	0.000
recruitment.YCS3	1.00000	1.00000	0.000
recruitment.YCS4	1.00000	1.00000	0.000
recruitment.YCS5	0.48497	0.46622	3.866
recruitment.YCS6	0.45827	0.45012	1.779
recruitment.YCS7	0.56856	0.56472	0.676
recruitment.YCS8	0.56672	0.56673	-0.001
recruitment.YCS9	0.48607	0.49069	-0.950
recruitment.YCS10	0.55503	0.56723	-2.198
recruitment.YCS11	0.56325	0.57884	-2.767
recruitment.YCS12	0.68756	0.71085	-3.387
recruitment.YCS13	0.62029	0.63612	-2.551
recruitment.YCS14	0.79057	0.80842	-2.257
recruitment.YCS15	0.46428	0.46926	-1.073
recruitment.YCS16	0.70075	0.70727	-0.929
recruitment.YCS17	0.41010	0.41046	-0.087
recruitment.YCS18	0.51501	0.51452	0.096
recruitment.YCS19	0.34165	0.34217	-0.154
recruitment.YCS20	0.34829	0.34726	0.295
recruitment.YCS21	0.43607	0.43820	-0.487
recruitment.YCS22	0.48058	0.47500	1.162
recruitment.YCS23	0.45216	0.45129	0.192
recruitment.YCS24	0.49168	0.49479	-0.631
recruitment.YCS25	0.46910	0.47066	-0.334
recruitment.YCS26	0.79927	0.80495	-0.710
recruitment.YCS27	0.79012	0.79211	-0.251
recruitment.YCS28	0.82606	0.83114	-0.615
recruitment.YCS29	0.70756	0.71251	-0.699
recruitment.YCS30	0.55170	0.55428	-0.468
recruitment.YCS31	0.47520	0.47677	-0.331
recruitment.YCS32	0.46170	0.46138	0.070
recruitment.YCS33	0.55496	0.55435	0.110
recruitment.YCS34	0.54666	0.54206	0.841
recruitment.YCS35	0.48323	0.48254	0.143
recruitment.YCS36	0.55016	0.54989	0.049
recruitment.YCS37	0.61527	0.61581	-0.087
recruitment.YCS38	0.77573	0.77473	0.129
recruitment.YCS39	0.63109	0.63059	0.080
recruitment.YCS40	0.77552	0.77349	0.262
recruitment.YCS41	0.64292	0.63935	0.555
recruitment.YCS42	0.70666	0.69938	1.030
recruitment.YCS43	0.65426	0.64860	0.864
recruitment.YCS44	0.50999	0.50618	0.746
recruitment.YCS45	0.58619	0.58729	-0.186
recruitment.YCS46	0.60348	0.58927	2.355
recruitment.YCS47	0.57681	0.57449	0.403

Casal2 parameter estimates

rownames	betadiff_casal_flags_on	betadiff_casal_flags_off	betadiff_casal_flags_on_low_tol	cppad_casal_flags_on	cppad_casal_flags_off	adolc_casal_flags_on	adolc_casal_flags_off	adolc_casal_flags_on_low_tol
process[Recruitment].b0	308529.000	308529.000	310577.000	310576.000	310576.000	308529.000	308529.000	310577.000
catchability[summerTANq].q	0.091	0.091	0.091	0.091	0.091	0.091	0.091	0.091
catchability[autumnTANq].q	0.126	0.126	0.126	0.126	0.126	0.126	0.126	0.126
selectivity[M_all].x0	12.496	12.496	12.984	12.984	12.984	12.496	12.496	12.984
selectivity[M_all].y0	0.133	0.133	0.128	0.128	0.128	0.133	0.133	0.128
selectivity[M_all].y1	0.383	0.383	0.447	0.447	0.447	0.383	0.383	0.447
selectivity[M_all].y2	0.351	0.351	0.354	0.354	0.354	0.351	0.351	0.354
selectivity[summerTANSel_m].a50	4.740	4.740	4.876	4.876	4.876	4.740	4.740	4.876
selectivity[summerTANSel_m].ato95	1.745	1.745	1.770	1.770	1.770	1.745	1.745	1.770
selectivity[summerTANSel_m].alpha	0.610	0.610	0.602	0.602	0.602	0.610	0.610	0.602
selectivity[summerTANSel_f].a50	5.461	5.461	5.608	5.608	5.608	5.461	5.461	5.608
selectivity[summerTANSel_f].ato95	2.203	2.203	2.214	2.214	2.214	2.203	2.203	2.214
selectivity[autumnTANSel_m].a50	5.510	5.510	5.640	5.640	5.640	5.510	5.510	5.640
selectivity[autumnTANSel_m].ato95	2.313	2.313	2.298	2.298	2.298	2.313	2.313	2.298
selectivity[autumnTANSel_m].alpha	0.942	0.942	0.933	0.933	0.933	0.942	0.942	0.933
selectivity[autumnTANSel_f].a50	5.916	5.916	6.058	6.058	6.058	5.916	5.916	6.058
selectivity[autumnTANSel_f].ato95	2.770	2.770	2.738	2.738	2.738	2.770	2.770	2.738
selectivity[trwlFSel_m].mu	8.369	8.369	8.402	8.402	8.402	8.369	8.369	8.402
selectivity[trwlFSel_m].sigma_l	1.970	1.970	1.947	1.947	1.947	1.970	1.970	1.947
selectivity[trwlFSel_m].sigma_r	61.523	61.523	200.000	200.000	200.000	61.523	61.523	200.000
selectivity[trwlFSel_m].alpha	1.043	1.043	1.021	1.021	1.021	1.043	1.043	1.021
selectivity[trwlFSel_f].mu	8.659	8.659	8.739	8.739	8.739	8.659	8.659	8.739
selectivity[trwlFSel_f].sigma_l	2.097	2.097	2.088	2.088	2.088	2.097	2.097	2.088
selectivity[trwlFSel_f].sigma_r	43.164	43.164	40.595	40.594	40.594	43.164	43.164	40.595
selectivity[lineHomeFSel_m].a50	11.456	11.456	8.608	8.608	8.608	11.456	11.456	8.608
selectivity[lineHomeFSel_m].ato95	8.600	8.600	4.592	4.592	4.592	8.600	8.600	4.592
selectivity[lineHomeFSel_m].alpha	0.380	0.380	0.270	0.270	0.270	0.380	0.380	0.270
selectivity[lineHomeFSel_f].a50	9.615	9.615	9.534	9.534	9.534	9.615	9.615	9.534
selectivity[lineHomeFSel_f].ato95	3.870	3.870	3.691	3.691	3.691	3.870	3.870	3.691
selectivity[lineSpawnFSel_m].a50	18.215	18.215	14.047	14.047	14.047	18.215	18.215	14.047
selectivity[lineSpawnFSel_m].ato95	13.600	13.600	10.026	10.026	10.026	13.600	13.600	10.026
selectivity[lineSpawnFSel_m].alpha	1.856	1.856	1.174	1.174	1.174	1.856	1.856	1.174
selectivity[lineSpawnFSel_f].a50	9.739	9.739	9.715	9.715	9.715	9.739	9.739	9.715
selectivity[lineSpawnFSel_f].ato95	2.994	2.994	2.897	2.897	2.897	2.994	2.994	2.897
process[Recruitment].ycs_values{1972}	0.484	0.484	0.466	0.466	0.466	0.484	0.484	0.466
process[Recruitment].ycs_values{1973}	0.461	0.461	0.450	0.450	0.450	0.461	0.461	0.450
process[Recruitment].ycs_values{1974}	0.568	0.568	0.565	0.565	0.565	0.568	0.568	0.565
process[Recruitment].ycs_values{1975}	0.567	0.567	0.567	0.567	0.567	0.567	0.567	0.567
process[Recruitment].ycs_values{1976}	0.486	0.486	0.491	0.491	0.491	0.486	0.486	0.491
process[Recruitment].ycs_values{1977}	0.554	0.554	0.567	0.567	0.567	0.554	0.554	0.567
process[Recruitment].ycs_values{1978}	0.563	0.563	0.579	0.579	0.579	0.563	0.563	0.579
process[Recruitment].ycs_values{1979}	0.689	0.689	0.711	0.711	0.711	0.689	0.689	0.711
process[Recruitment].ycs_values{1980}	0.621	0.621	0.636	0.636	0.636	0.621	0.621	0.636
process[Recruitment].ycs_values{1981}	0.792	0.792	0.808	0.808	0.808	0.792	0.792	0.808
process[Recruitment].ycs_values{1982}	0.465	0.465	0.469	0.469	0.469	0.465	0.465	0.469
process[Recruitment].ycs_values{1983}	0.700	0.700	0.707	0.707	0.707	0.700	0.700	0.707
process[Recruitment].ycs_values{1984}	0.410	0.410	0.410	0.410	0.410	0.410	0.410	0.410
process[Recruitment].ycs_values{1985}	0.515	0.515	0.515	0.515	0.515	0.515	0.515	0.515
process[Recruitment].ycs_values{1986}	0.341	0.341	0.342	0.342	0.342	0.341	0.341	0.342
process[Recruitment].ycs_values{1987}	0.348	0.348	0.347	0.347	0.347	0.348	0.348	0.347
process[Recruitment].ycs_values{1988}	0.438	0.438	0.438	0.438	0.438	0.438	0.438	0.438
process[Recruitment].ycs_values{1989}	0.479	0.479	0.475	0.475	0.475	0.479	0.479	0.475
process[Recruitment].ycs_values{1990}	0.452	0.452	0.451	0.451	0.451	0.452	0.452	0.451
process[Recruitment].ycs_values{1991}	0.493	0.493	0.495	0.495	0.495	0.493	0.493	0.495
process[Recruitment].ycs_values{1992}	0.469	0.469	0.471	0.471	0.471	0.469	0.469	0.471
process[Recruitment].ycs_values{1993}	0.798	0.798	0.805	0.805	0.805	0.798	0.798	0.805
process[Recruitment].ycs_values{1994}	0.791	0.791	0.792	0.792	0.792	0.791	0.791	0.792
process[Recruitment].ycs_values{1995}	0.825	0.825	0.831	0.831	0.831	0.825	0.825	0.831
process[Recruitment].ycs_values{1996}	0.707	0.707	0.712	0.712	0.712	0.707	0.707	0.712
process[Recruitment].ycs_values{1997}	0.552	0.552	0.554	0.554	0.554	0.552	0.552	0.554
process[Recruitment].ycs_values{1998}	0.475	0.475	0.477	0.477	0.477	0.475	0.475	0.477
process[Recruitment].ycs_values{1999}	0.461	0.461	0.461	0.461	0.461	0.461	0.461	0.461
process[Recruitment].ycs_values{2000}	0.556	0.556	0.554	0.554	0.554	0.556	0.556	0.554
process[Recruitment].ycs_values{2001}	0.545	0.545	0.542	0.542	0.542	0.545	0.545	0.542
process[Recruitment].ycs_values{2002}	0.484	0.484	0.483	0.483	0.483	0.484	0.484	0.483
process[Recruitment].ycs_values{2003}	0.550	0.550	0.550	0.550	0.550	0.550	0.550	0.550
process[Recruitment].ycs_values{2004}	0.614	0.614	0.616	0.616	0.616	0.614	0.614	0.616
process[Recruitment].ycs_values{2005}	0.777	0.777	0.775	0.775	0.775	0.777	0.777	0.775
process[Recruitment].ycs_values{2006}	0.631	0.631	0.631	0.631	0.631	0.631	0.631	0.631
process[Recruitment].ycs_values{2007}	0.774	0.774	0.773	0.773	0.773	0.774	0.774	0.773
process[Recruitment].ycs_values{2008}	0.643	0.643	0.639	0.639	0.639	0.643	0.643	0.639
process[Recruitment].ycs_values{2009}	0.706	0.706	0.699	0.699	0.699	0.706	0.706	0.699
process[Recruitment].ycs_values{2010}	0.653	0.653	0.649	0.649	0.649	0.653	0.653	0.649
process[Recruitment].ycs_values{2011}	0.511	0.511	0.506	0.506	0.506	0.511	0.511	0.506
process[Recruitment].ycs_values{2012}	0.586	0.586	0.587	0.587	0.587	0.586	0.586	0.587
process[Recruitment].ycs_values{2013}	0.601	0.601	0.589	0.589	0.589	0.601	0.601	0.589
process[Recruitment].ycs_values{2014}	0.576	0.576	0.574	0.574	0.574	0.576	0.576	0.574

Casal2 parameter estimates: Percent Difference from betadiff_casal_flags_on

rownames	betadiff_casal_flags_on	betadiff_casal_flags_off	betadiff_casal_flags_on_low_tol	cppad_casal_flags_on	cppad_casal_flags_off	adolc_casal_flags_on	adolc_casal_flags_off	adolc_casal_flags_on_low_tol
process[Recruitment].b0	0.000	0.000	-0.664	-0.663	-0.663	0.000	0.000	-0.664
catchability[summerTANq].q	0.000	0.000	0.344	0.344	0.344	0.000	0.000	0.344
catchability[autumnTANq].q	0.000	0.000	0.105	0.105	0.105	0.000	0.000	0.105
selectivity[M_all].x0	0.000	0.000	-3.904	-3.904	-3.904	0.000	0.000	-3.904
selectivity[M_all].y0	0.000	0.000	3.510	3.510	3.510	0.000	0.000	3.510
selectivity[M_all].y1	0.000	0.000	-16.840	-16.841	-16.841	0.000	0.000	-16.840
selectivity[M_all].y2	0.000	0.000	-0.741	-0.740	-0.740	0.000	0.000	-0.741
selectivity[summerTANSel_m].a50	0.000	0.000	-2.881	-2.882	-2.882	0.000	0.000	-2.881
selectivity[summerTANSel_m].ato95	0.000	0.000	-1.473	-1.473	-1.473	0.000	0.000	-1.473
selectivity[summerTANSel_m].alpha	0.000	0.000	1.329	1.329	1.329	0.000	0.000	1.329
selectivity[summerTANSel_f].a50	0.000	0.000	-2.691	-2.691	-2.691	0.000	0.000	-2.691
selectivity[summerTANSel_f].ato95	0.000	0.000	-0.490	-0.490	-0.490	0.000	0.000	-0.490
selectivity[autumnTANSel_m].a50	0.000	0.000	-2.358	-2.358	-2.358	0.000	0.000	-2.358
selectivity[autumnTANSel_m].ato95	0.000	0.000	0.644	0.644	0.644	0.000	0.000	0.644
selectivity[autumnTANSel_m].alpha	0.000	0.000	0.906	0.907	0.907	0.000	0.000	0.906
selectivity[autumnTANSel_f].a50	0.000	0.000	-2.413	-2.413	-2.413	0.000	0.000	-2.413
selectivity[autumnTANSel_f].ato95	0.000	0.000	1.146	1.146	1.146	0.000	0.000	1.146
selectivity[trwlFSel_m].mu	0.000	0.000	-0.397	-0.397	-0.397	0.000	0.000	-0.397
selectivity[trwlFSel_m].sigma_l	0.000	0.000	1.161	1.161	1.161	0.000	0.000	1.161
selectivity[trwlFSel_m].sigma_r	0.000	0.000	-225.082	-225.082	-225.082	0.000	0.000	-225.082
selectivity[trwlFSel_m].alpha	0.000	0.000	2.101	2.101	2.101	0.000	0.000	2.101
selectivity[trwlFSel_f].mu	0.000	0.000	-0.935	-0.935	-0.935	0.000	0.000	-0.935
selectivity[trwlFSel_f].sigma_l	0.000	0.000	0.385	0.385	0.385	0.000	0.000	0.385
selectivity[trwlFSel_f].sigma_r	0.000	0.000	5.952	5.954	5.954	0.000	0.000	5.952
selectivity[lineHomeFSel_m].a50	0.000	0.000	24.857	24.858	24.858	0.000	0.000	24.857
selectivity[lineHomeFSel_m].ato95	0.000	0.000	46.606	46.607	46.607	0.000	0.000	46.606
selectivity[lineHomeFSel_m].alpha	0.000	0.000	29.007	29.008	29.008	0.000	0.000	29.007
selectivity[lineHomeFSel_f].a50	0.000	0.000	0.845	0.845	0.845	0.000	0.000	0.845
selectivity[lineHomeFSel_f].ato95	0.000	0.000	4.638	4.638	4.638	0.000	0.000	4.638
selectivity[lineSpawnFSel_m].a50	0.000	0.000	22.884	22.884	22.884	0.000	0.000	22.884
selectivity[lineSpawnFSel_m].ato95	0.000	0.000	26.276	26.277	26.277	0.000	0.000	26.276
selectivity[lineSpawnFSel_m].alpha	0.000	0.000	36.731	36.731	36.731	0.000	0.000	36.731
selectivity[lineSpawnFSel_f].a50	0.000	0.000	0.245	0.245	0.245	0.000	0.000	0.245
selectivity[lineSpawnFSel_f].ato95	0.000	0.000	3.246	3.246	3.246	0.000	0.000	3.246
process[Recruitment].ycs_values{1972}	0.000	0.000	3.589	3.589	3.589	0.000	0.000	3.589
process[Recruitment].ycs_values{1973}	0.000	0.000	2.389	2.389	2.389	0.000	0.000	2.389
process[Recruitment].ycs_values{1974}	0.000	0.000	0.675	0.675	0.675	0.000	0.000	0.675
process[Recruitment].ycs_values{1975}	0.000	0.000	-0.064	-0.064	-0.064	0.000	0.000	-0.064
process[Recruitment].ycs_values{1976}	0.000	0.000	-0.916	-0.916	-0.916	0.000	0.000	-0.916
process[Recruitment].ycs_values{1977}	0.000	0.000	-2.353	-2.353	-2.353	0.000	0.000	-2.353
process[Recruitment].ycs_values{1978}	0.000	0.000	-2.733	-2.732	-2.732	0.000	0.000	-2.733
process[Recruitment].ycs_values{1979}	0.000	0.000	-3.185	-3.185	-3.185	0.000	0.000	-3.185
process[Recruitment].ycs_values{1980}	0.000	0.000	-2.457	-2.457	-2.457	0.000	0.000	-2.457
process[Recruitment].ycs_values{1981}	0.000	0.000	-1.962	-1.962	-1.962	0.000	0.000	-1.962
process[Recruitment].ycs_values{1982}	0.000	0.000	-0.906	-0.906	-0.906	0.000	0.000	-0.906
process[Recruitment].ycs_values{1983}	0.000	0.000	-1.056	-1.056	-1.056	0.000	0.000	-1.056
process[Recruitment].ycs_values{1984}	0.000	0.000	-0.115	-0.115	-0.115	0.000	0.000	-0.115
process[Recruitment].ycs_values{1985}	0.000	0.000	0.162	0.162	0.162	0.000	0.000	0.162
process[Recruitment].ycs_values{1986}	0.000	0.000	-0.236	-0.235	-0.235	0.000	0.000	-0.236
process[Recruitment].ycs_values{1987}	0.000	0.000	0.091	0.091	0.091	0.000	0.000	0.091
process[Recruitment].ycs_values{1988}	0.000	0.000	-0.079	-0.078	-0.078	0.000	0.000	-0.079
process[Recruitment].ycs_values{1989}	0.000	0.000	0.884	0.885	0.885	0.000	0.000	0.884
process[Recruitment].ycs_values{1990}	0.000	0.000	0.106	0.106	0.106	0.000	0.000	0.106
process[Recruitment].ycs_values{1991}	0.000	0.000	-0.436	-0.436	-0.436	0.000	0.000	-0.436
process[Recruitment].ycs_values{1992}	0.000	0.000	-0.325	-0.325	-0.325	0.000	0.000	-0.325
process[Recruitment].ycs_values{1993}	0.000	0.000	-0.871	-0.871	-0.871	0.000	0.000	-0.871
process[Recruitment].ycs_values{1994}	0.000	0.000	-0.102	-0.102	-0.102	0.000	0.000	-0.102
process[Recruitment].ycs_values{1995}	0.000	0.000	-0.691	-0.691	-0.691	0.000	0.000	-0.691
process[Recruitment].ycs_values{1996}	0.000	0.000	-0.736	-0.736	-0.736	0.000	0.000	-0.736
process[Recruitment].ycs_values{1997}	0.000	0.000	-0.400	-0.400	-0.400	0.000	0.000	-0.400
process[Recruitment].ycs_values{1998}	0.000	0.000	-0.368	-0.368	-0.368	0.000	0.000	-0.368
process[Recruitment].ycs_values{1999}	0.000	0.000	-0.045	-0.045	-0.045	0.000	0.000	-0.045
process[Recruitment].ycs_values{2000}	0.000	0.000	0.239	0.239	0.239	0.000	0.000	0.239
process[Recruitment].ycs_values{2001}	0.000	0.000	0.623	0.623	0.623	0.000	0.000	0.623
process[Recruitment].ycs_values{2002}	0.000	0.000	0.227	0.227	0.227	0.000	0.000	0.227
process[Recruitment].ycs_values{2003}	0.000	0.000	-0.008	-0.007	-0.007	0.000	0.000	-0.008
process[Recruitment].ycs_values{2004}	0.000	0.000	-0.260	-0.260	-0.260	0.000	0.000	-0.260
process[Recruitment].ycs_values{2005}	0.000	0.000	0.321	0.321	0.321	0.000	0.000	0.321
process[Recruitment].ycs_values{2006}	0.000	0.000	0.123	0.124	0.124	0.000	0.000	0.123
process[Recruitment].ycs_values{2007}	0.000	0.000	0.042	0.042	0.042	0.000	0.000	0.042
process[Recruitment].ycs_values{2008}	0.000	0.000	0.503	0.503	0.503	0.000	0.000	0.503
process[Recruitment].ycs_values{2009}	0.000	0.000	1.010	1.010	1.010	0.000	0.000	1.010
process[Recruitment].ycs_values{2010}	0.000	0.000	0.674	0.675	0.675	0.000	0.000	0.674
process[Recruitment].ycs_values{2011}	0.000	0.000	1.004	1.004	1.004	0.000	0.000	1.004
process[Recruitment].ycs_values{2012}	0.000	0.000	-0.311	-0.311	-0.311	0.000	0.000	-0.311
process[Recruitment].ycs_values{2013}	0.000	0.000	1.918	1.919	1.919	0.000	0.000	1.918
process[Recruitment].ycs_values{2014}	0.000	0.000	0.262	0.265	0.265	0.000	0.000	0.262

CASAL objective function component values

Component	Base_Model	Sensitivity_1
Tangaroa_bio_autumn	-6.829	-6.834
Tangaroa_bio_summer	-23.884	-23.962
Tangaroa_propn_at_age_aut	175.718	175.789
Tangaroa_propn_at_age_summer	835.903	835.602
longline_Campbell_home_propn_at_age	275.676	275.416
longline_Puysegur_spawn_propn_at_age	363.279	363.252
trawl_observer_propn_at_age	682.612	682.293
prior_on_q[tan_sum].q	-2.364	-2.366
prior_on_q[tan_aut].q	-2.033	-2.037
prior_on_initialization.B0	12.641	12.646
prior_on_natural_mortality.ogive_all	0.000	0.000
prior_on_selectivity[surveysum_sel].male	0.000	0.000
prior_on_selectivity[surveysum_sel].female	0.000	0.000
prior_on_selectivity[surveyaut_sel].male	0.000	0.000
prior_on_selectivity[surveyaut_sel].female	0.000	0.000
prior_on_selectivity[trawl_sel].male	0.000	0.000
prior_on_selectivity[trawl_sel].female	0.000	0.000
prior_on_selectivity[line_home_sel].male	0.000	0.000
prior_on_selectivity[line_home_sel].female	0.000	0.000
prior_on_selectivity[line_spawn_sel].male	0.000	0.000
prior_on_selectivity[line_spawn_sel].female	0.000	0.000
prior_on_recruitment.YCS	-14.441	-14.366
clp1	0.000	0.000
clp2	0.000	0.000
clp3	0.000	0.000
YCS_average_1	0.908	0.903
Total	2297.190	2296.340

Casal2 objective function component values

rownames	betadiff_casal_flags_on	betadiff_casal_flags_off	betadiff_casal_flags_on_low_tol	cppad_casal_flags_on	cppad_casal_flags_off	adolc_casal_flags_on	adolc_casal_flags_off	adolc_casal_flags_on_low_tol
observation->summerTANbiomass-1992	-1.693	-1.693	-1.679	-1.679	-1.679	-1.693	-1.693	-1.679
observation->summerTANbiomass-1993	-1.353	-1.353	-1.331	-1.331	-1.331	-1.353	-1.353	-1.331
observation->summerTANbiomass-1994	-0.975	-0.975	-0.991	-0.991	-0.991	-0.975	-0.975	-0.991
observation->summerTANbiomass-2001	0.430	0.430	0.354	0.354	0.354	0.430	0.430	0.354
observation->summerTANbiomass-2002	-1.778	-1.778	-1.786	-1.786	-1.786	-1.778	-1.778	-1.786
observation->summerTANbiomass-2003	-1.685	-1.685	-1.693	-1.693	-1.693	-1.685	-1.685	-1.693
observation->summerTANbiomass-2004	-1.598	-1.598	-1.586	-1.586	-1.586	-1.598	-1.598	-1.586
observation->summerTANbiomass-2005	-1.657	-1.657	-1.656	-1.656	-1.656	-1.657	-1.657	-1.656
observation->summerTANbiomass-2006	-1.143	-1.143	-1.153	-1.153	-1.153	-1.143	-1.143	-1.153
observation->summerTANbiomass-2007	-1.162	-1.162	-1.180	-1.180	-1.180	-1.162	-1.162	-1.180
observation->summerTANbiomass-2008	-1.568	-1.568	-1.553	-1.553	-1.553	-1.568	-1.568	-1.553
observation->summerTANbiomass-2009	-1.700	-1.700	-1.705	-1.705	-1.705	-1.700	-1.700	-1.705
observation->summerTANbiomass-2010	-1.672	-1.672	-1.678	-1.678	-1.678	-1.672	-1.672	-1.678
observation->summerTANbiomass-2012	-1.554	-1.554	-1.558	-1.558	-1.558	-1.554	-1.554	-1.558
observation->summerTANbiomass-2013	-1.669	-1.669	-1.667	-1.667	-1.667	-1.669	-1.669	-1.667
observation->summerTANbiomass-2015	-1.582	-1.582	-1.570	-1.570	-1.570	-1.582	-1.582	-1.570
observation->summerTANbiomass-2017	-1.526	-1.526	-1.528	-1.528	-1.528	-1.526	-1.526	-1.528
observation->Tangaroa_propn_at_age_summer-1990	44.218	44.218	44.393	44.393	44.393	44.218	44.218	44.393
observation->Tangaroa_propn_at_age_summer-1992	51.993	51.993	51.753	51.753	51.753	51.993	51.993	51.753
observation->Tangaroa_propn_at_age_summer-1993	50.200	50.200	50.168	50.168	50.168	50.200	50.200	50.168
observation->Tangaroa_propn_at_age_summer-1994	49.743	49.743	49.785	49.785	49.785	49.743	49.743	49.785
observation->Tangaroa_propn_at_age_summer-2001	48.355	48.355	48.237	48.237	48.237	48.355	48.355	48.237
observation->Tangaroa_propn_at_age_summer-2002	47.830	47.830	47.879	47.879	47.879	47.830	47.830	47.879
observation->Tangaroa_propn_at_age_summer-2003	48.442	48.442	48.620	48.620	48.620	48.442	48.442	48.620
observation->Tangaroa_propn_at_age_summer-2004	44.823	44.823	44.865	44.865	44.865	44.823	44.823	44.865
observation->Tangaroa_propn_at_age_summer-2005	43.097	43.097	43.117	43.117	43.117	43.097	43.097	43.117
observation->Tangaroa_propn_at_age_summer-2006	43.891	43.891	44.058	44.058	44.058	43.891	43.891	44.058
observation->Tangaroa_propn_at_age_summer-2007	41.848	41.848	41.841	41.841	41.841	41.848	41.848	41.841
observation->Tangaroa_propn_at_age_summer-2008	45.225	45.225	45.267	45.267	45.267	45.225	45.225	45.267
observation->Tangaroa_propn_at_age_summer-2009	46.844	46.844	46.806	46.806	46.806	46.844	46.844	46.806
observation->Tangaroa_propn_at_age_summer-2010	47.128	47.128	47.202	47.202	47.202	47.128	47.128	47.202
observation->Tangaroa_propn_at_age_summer-2012	44.353	44.353	44.183	44.183	44.183	44.353	44.353	44.183
observation->Tangaroa_propn_at_age_summer-2013	47.251	47.251	47.021	47.021	47.021	47.251	47.251	47.021
observation->Tangaroa_propn_at_age_summer-2015	46.473	46.473	46.342	46.342	46.342	46.473	46.473	46.342
observation->Tangaroa_propn_at_age_summer-2017	44.182	44.182	44.082	44.082	44.082	44.182	44.182	44.082
observation->autumnTANbiomass-1992	-1.558	-1.558	-1.572	-1.572	-1.572	-1.558	-1.558	-1.572
observation->autumnTANbiomass-1993	-1.741	-1.741	-1.733	-1.733	-1.733	-1.741	-1.741	-1.733
observation->autumnTANbiomass-1996	-1.779	-1.779	-1.779	-1.779	-1.779	-1.779	-1.779	-1.779
observation->autumnTANbiomass-1998	-1.750	-1.750	-1.750	-1.750	-1.750	-1.750	-1.750	-1.750
observation->Tangaroa_propn_at_age_autumn-1992	44.589	44.589	44.443	44.443	44.443	44.589	44.589	44.443
observation->Tangaroa_propn_at_age_autumn-1993	45.484	45.484	45.443	45.443	45.443	45.484	45.484	45.443
observation->Tangaroa_propn_at_age_autumn-1996	42.184	42.184	42.295	42.295	42.295	42.184	42.184	42.295
observation->Tangaroa_propn_at_age_autumn-1998	43.464	43.464	43.610	43.610	43.610	43.464	43.464	43.610
observation->trawl_propn_at_age-1992	36.067	36.067	35.944	35.944	35.944	36.067	36.067	35.944
observation->trawl_propn_at_age-1993	27.516	27.516	27.476	27.476	27.476	27.516	27.516	27.476
observation->trawl_propn_at_age-1994	25.819	25.819	25.764	25.764	25.764	25.819	25.819	25.764
observation->trawl_propn_at_age-1996	28.394	28.394	28.397	28.397	28.397	28.394	28.394	28.397
observation->trawl_propn_at_age-1998	24.915	24.915	24.910	24.910	24.910	24.915	24.915	24.910
observation->trawl_propn_at_age-2001	24.580	24.580	24.542	24.542	24.542	24.580	24.580	24.542
observation->trawl_propn_at_age-2002	26.770	26.770	26.792	26.792	26.792	26.770	26.770	26.792
observation->trawl_propn_at_age-2003	34.564	34.564	34.511	34.511	34.511	34.564	34.564	34.511
observation->trawl_propn_at_age-2004	29.608	29.608	29.608	29.608	29.608	29.608	29.608	29.608
observation->trawl_propn_at_age-2005	30.147	30.147	30.166	30.166	30.166	30.147	30.147	30.166
observation->trawl_propn_at_age-2006	33.629	33.629	33.714	33.714	33.714	33.629	33.629	33.714
observation->trawl_propn_at_age-2007	26.635	26.635	26.588	26.588	26.588	26.635	26.635	26.588
observation->trawl_propn_at_age-2008	27.059	27.059	27.076	27.076	27.076	27.059	27.059	27.076
observation->trawl_propn_at_age-2009	37.213	37.213	37.237	37.237	37.237	37.213	37.213	37.237
observation->trawl_propn_at_age-2010	30.648	30.648	30.694	30.694	30.694	30.648	30.648	30.694
observation->trawl_propn_at_age-2011	31.266	31.266	31.260	31.260	31.260	31.266	31.266	31.260
observation->trawl_propn_at_age-2012	32.325	32.325	32.366	32.366	32.366	32.325	32.325	32.366
observation->trawl_propn_at_age-2013	37.072	37.072	36.943	36.943	36.943	37.072	37.072	36.943
observation->trawl_propn_at_age-2014	30.640	30.640	30.642	30.642	30.642	30.640	30.640	30.642
observation->trawl_propn_at_age-2015	33.456	33.456	33.474	33.474	33.474	33.456	33.456	33.474
observation->trawl_propn_at_age-2016	36.532	36.532	36.482	36.482	36.482	36.532	36.532	36.482
observation->trawl_propn_at_age-2017	37.755	37.755	37.708	37.708	37.708	37.755	37.755	37.708
observation->longline_Campbell_home_propn_at_age-1999	45.348	45.348	45.256	45.256	45.256	45.348	45.348	45.256
observation->longline_Campbell_home_propn_at_age-2001	31.965	31.965	31.950	31.950	31.950	31.965	31.965	31.950
observation->longline_Campbell_home_propn_at_age-2003	28.644	28.644	28.675	28.675	28.675	28.644	28.644	28.675
observation->longline_Campbell_home_propn_at_age-2005	32.750	32.750	32.776	32.776	32.776	32.750	32.750	32.776
observation->longline_Campbell_home_propn_at_age-2009	26.033	26.033	25.611	25.611	25.611	26.033	26.033	25.611
observation->longline_Campbell_home_propn_at_age-2010	24.302	24.302	24.461	24.461	24.461	24.302	24.302	24.461
observation->longline_Campbell_home_propn_at_age-2011	28.878	28.878	28.935	28.935	28.935	28.878	28.878	28.935
observation->longline_Campbell_home_propn_at_age-2012	32.258	32.258	32.389	32.389	32.389	32.258	32.258	32.389
observation->longline_Campbell_home_propn_at_age-2014	25.495	25.495	25.357	25.357	25.357	25.495	25.495	25.357
observation->longline_Puyseger_home_propn_at_age-2000	42.745	42.745	42.680	42.680	42.680	42.745	42.745	42.680
observation->longline_Puyseger_home_propn_at_age-2001	31.770	31.770	31.900	31.900	31.900	31.770	31.770	31.900
observation->longline_Puyseger_home_propn_at_age-2002	39.978	39.978	39.998	39.998	39.998	39.978	39.978	39.998
observation->longline_Puyseger_home_propn_at_age-2003	43.527	43.527	43.511	43.511	43.511	43.527	43.527	43.511
observation->longline_Puyseger_home_propn_at_age-2004	39.957	39.957	40.015	40.015	40.015	39.957	39.957	40.015
observation->longline_Puyseger_home_propn_at_age-2005	25.532	25.532	25.358	25.358	25.358	25.532	25.532	25.358
observation->longline_Puyseger_home_propn_at_age-2006	35.210	35.210	35.426	35.426	35.426	35.210	35.210	35.426
observation->longline_Puyseger_home_propn_at_age-2007	33.981	33.981	33.782	33.782	33.782	33.981	33.981	33.782
observation->longline_Puyseger_home_propn_at_age-2008	19.139	19.139	19.113	19.113	19.113	19.139	19.139	19.113
observation->longline_Puyseger_home_propn_at_age-2010	24.238	24.238	24.366	24.366	24.366	24.238	24.238	24.366
observation->longline_Puyseger_home_propn_at_age-2017	27.200	27.200	27.093	27.093	27.093	27.200	27.200	27.093
prior->B0->process[Recruitment].b0	12.640	12.640	12.646	12.646	12.646	12.640	12.640	12.646
prior->summerTANq->catchability[summerTANq].q	-2.363	-2.363	-2.365	-2.365	-2.365	-2.363	-2.363	-2.365
prior->autumnTANq->catchability[autumnTANq].q	-2.035	-2.035	-2.037	-2.037	-2.037	-2.035	-2.035	-2.037
prior->M_all_x0->selectivity[M_all].x0	0.000	0.000	0.000	0.000	0.000	0.000	0.000	0.000
prior->M_all_y0->selectivity[M_all].y0	0.000	0.000	0.000	0.000	0.000	0.000	0.000	0.000
prior->M_all_y1->selectivity[M_all].y1	0.000	0.000	0.000	0.000	0.000	0.000	0.000	0.000
prior->M_all_y2->selectivity[M_all].y2	0.000	0.000	0.000	0.000	0.000	0.000	0.000	0.000
prior->selectivity[summerTANSel_m].a50	0.000	0.000	0.000	0.000	0.000	0.000	0.000	0.000
prior->selectivity[summerTANSel_m].ato95	0.000	0.000	0.000	0.000	0.000	0.000	0.000	0.000
prior->selectivity[summerTANSel_m].alpha	0.000	0.000	0.000	0.000	0.000	0.000	0.000	0.000
prior->selectivity[summerTANSel_f].a50	0.000	0.000	0.000	0.000	0.000	0.000	0.000	0.000
prior->selectivity[summerTANSel_f].ato95	0.000	0.000	0.000	0.000	0.000	0.000	0.000	0.000
prior->selectivity[autumnTANSel_m].a50	0.000	0.000	0.000	0.000	0.000	0.000	0.000	0.000
prior->selectivity[autumnTANSel_m].ato95	0.000	0.000	0.000	0.000	0.000	0.000	0.000	0.000
prior->selectivity[autumnTANSel_m].alpha	0.000	0.000	0.000	0.000	0.000	0.000	0.000	0.000
prior->selectivity[autumnTANSel_f].a50	0.000	0.000	0.000	0.000	0.000	0.000	0.000	0.000
prior->selectivity[autumnTANSel_f].ato95	0.000	0.000	0.000	0.000	0.000	0.000	0.000	0.000
prior->selectivity[trwlFSel_m].mu	0.000	0.000	0.000	0.000	0.000	0.000	0.000	0.000
prior->selectivity[trwlFSel_m].sigma_l	0.000	0.000	0.000	0.000	0.000	0.000	0.000	0.000
prior->selectivity[trwlFSel_m].sigma_r	0.000	0.000	0.000	0.000	0.000	0.000	0.000	0.000
prior->selectivity[trwlFSel_m].alpha	0.000	0.000	0.000	0.000	0.000	0.000	0.000	0.000
prior->selectivity[trwlFSel_f].mu	0.000	0.000	0.000	0.000	0.000	0.000	0.000	0.000
prior->selectivity[trwlFSel_f].sigma_l	0.000	0.000	0.000	0.000	0.000	0.000	0.000	0.000
prior->selectivity[trwlFSel_f].sigma_r	0.000	0.000	0.000	0.000	0.000	0.000	0.000	0.000
prior->selectivity[lineHomeFSel_m].a50	0.000	0.000	0.000	0.000	0.000	0.000	0.000	0.000
prior->selectivity[lineHomeFSel_m].ato95	0.000	0.000	0.000	0.000	0.000	0.000	0.000	0.000
prior->selectivity[lineHomeFSel_m].alpha	0.000	0.000	0.000	0.000	0.000	0.000	0.000	0.000
prior->selectivity[lineHomeFSel_f].a50	0.000	0.000	0.000	0.000	0.000	0.000	0.000	0.000
prior->selectivity[lineHomeFSel_f].ato95	0.000	0.000	0.000	0.000	0.000	0.000	0.000	0.000
prior->selectivity[lineSpawnFSel_m].a50	0.000	0.000	0.000	0.000	0.000	0.000	0.000	0.000
prior->selectivity[lineSpawnFSel_m].ato95	0.000	0.000	0.000	0.000	0.000	0.000	0.000	0.000
prior->selectivity[lineSpawnFSel_m].alpha	0.000	0.000	0.000	0.000	0.000	0.000	0.000	0.000
prior->selectivity[lineSpawnFSel_f].a50	0.000	0.000	0.000	0.000	0.000	0.000	0.000	0.000
prior->selectivity[lineSpawnFSel_f].ato95	0.000	0.000	0.000	0.000	0.000	0.000	0.000	0.000
prior->process[Recruitment].ycs_values{1972}	-0.378	-0.378	-0.365	-0.365	-0.365	-0.378	-0.378	-0.365
prior->process[Recruitment].ycs_values{1973}	-0.360	-0.360	-0.349	-0.349	-0.349	-0.360	-0.360	-0.349
prior->process[Recruitment].ycs_values{1974}	-0.397	-0.397	-0.398	-0.398	-0.398	-0.397	-0.397	-0.398
prior->process[Recruitment].ycs_values{1975}	-0.398	-0.398	-0.398	-0.398	-0.398	-0.398	-0.398	-0.398
prior->process[Recruitment].ycs_values{1976}	-0.380	-0.380	-0.383	-0.383	-0.383	-0.380	-0.380	-0.383
prior->process[Recruitment].ycs_values{1977}	-0.399	-0.399	-0.398	-0.398	-0.398	-0.399	-0.399	-0.398
prior->process[Recruitment].ycs_values{1978}	-0.398	-0.398	-0.396	-0.396	-0.396	-0.398	-0.398	-0.396
prior->process[Recruitment].ycs_values{1979}	-0.335	-0.335	-0.316	-0.316	-0.316	-0.335	-0.335	-0.316
prior->process[Recruitment].ycs_values{1980}	-0.380	-0.380	-0.372	-0.372	-0.372	-0.380	-0.380	-0.372
prior->process[Recruitment].ycs_values{1981}	-0.231	-0.231	-0.213	-0.213	-0.213	-0.231	-0.231	-0.213
prior->process[Recruitment].ycs_values{1982}	-0.364	-0.364	-0.367	-0.367	-0.367	-0.364	-0.364	-0.367
prior->process[Recruitment].ycs_values{1983}	-0.326	-0.326	-0.319	-0.319	-0.319	-0.326	-0.326	-0.319
prior->process[Recruitment].ycs_values{1984}	-0.291	-0.291	-0.292	-0.292	-0.292	-0.291	-0.291	-0.292
prior->process[Recruitment].ycs_values{1985}	-0.394	-0.394	-0.393	-0.393	-0.393	-0.394	-0.394	-0.393
prior->process[Recruitment].ycs_values{1986}	-0.114	-0.114	-0.117	-0.117	-0.117	-0.114	-0.114	-0.117
prior->process[Recruitment].ycs_values{1987}	-0.135	-0.135	-0.134	-0.134	-0.134	-0.135	-0.135	-0.134
prior->process[Recruitment].ycs_values{1988}	-0.334	-0.334	-0.334	-0.334	-0.334	-0.334	-0.334	-0.334
prior->process[Recruitment].ycs_values{1989}	-0.375	-0.375	-0.372	-0.372	-0.372	-0.375	-0.375	-0.372
prior->process[Recruitment].ycs_values{1990}	-0.350	-0.350	-0.350	-0.350	-0.350	-0.350	-0.350	-0.350
prior->process[Recruitment].ycs_values{1991}	-0.384	-0.384	-0.385	-0.385	-0.385	-0.384	-0.384	-0.385
prior->process[Recruitment].ycs_values{1992}	-0.367	-0.367	-0.369	-0.369	-0.369	-0.367	-0.367	-0.369
prior->process[Recruitment].ycs_values{1993}	-0.225	-0.225	-0.217	-0.217	-0.217	-0.225	-0.225	-0.217
prior->process[Recruitment].ycs_values{1994}	-0.233	-0.233	-0.232	-0.232	-0.232	-0.233	-0.233	-0.232
prior->process[Recruitment].ycs_values{1995}	-0.192	-0.192	-0.185	-0.185	-0.185	-0.192	-0.192	-0.185
prior->process[Recruitment].ycs_values{1996}	-0.319	-0.319	-0.315	-0.315	-0.315	-0.319	-0.319	-0.315
prior->process[Recruitment].ycs_values{1997}	-0.399	-0.399	-0.399	-0.399	-0.399	-0.399	-0.399	-0.399
prior->process[Recruitment].ycs_values{1998}	-0.372	-0.372	-0.373	-0.373	-0.373	-0.372	-0.372	-0.373
prior->process[Recruitment].ycs_values{1999}	-0.360	-0.360	-0.360	-0.360	-0.360	-0.360	-0.360	-0.360
prior->process[Recruitment].ycs_values{2000}	-0.399	-0.399	-0.399	-0.399	-0.399	-0.399	-0.399	-0.399
prior->process[Recruitment].ycs_values{2001}	-0.399	-0.399	-0.399	-0.399	-0.399	-0.399	-0.399	-0.399
prior->process[Recruitment].ycs_values{2002}	-0.378	-0.378	-0.377	-0.377	-0.377	-0.378	-0.378	-0.377
prior->process[Recruitment].ycs_values{2003}	-0.399	-0.399	-0.399	-0.399	-0.399	-0.399	-0.399	-0.399
prior->process[Recruitment].ycs_values{2004}	-0.383	-0.383	-0.383	-0.383	-0.383	-0.383	-0.383	-0.383
prior->process[Recruitment].ycs_values{2005}	-0.249	-0.249	-0.251	-0.251	-0.251	-0.249	-0.249	-0.251
prior->process[Recruitment].ycs_values{2006}	-0.375	-0.375	-0.375	-0.375	-0.375	-0.375	-0.375	-0.375
prior->process[Recruitment].ycs_values{2007}	-0.252	-0.252	-0.253	-0.253	-0.253	-0.252	-0.252	-0.253
prior->process[Recruitment].ycs_values{2008}	-0.368	-0.368	-0.370	-0.370	-0.370	-0.368	-0.368	-0.370
prior->process[Recruitment].ycs_values{2009}	-0.320	-0.320	-0.326	-0.326	-0.326	-0.320	-0.320	-0.326
prior->process[Recruitment].ycs_values{2010}	-0.362	-0.362	-0.364	-0.364	-0.364	-0.362	-0.362	-0.364
prior->process[Recruitment].ycs_values{2011}	-0.392	-0.392	-0.390	-0.390	-0.390	-0.392	-0.392	-0.390
prior->process[Recruitment].ycs_values{2012}	-0.394	-0.394	-0.393	-0.393	-0.393	-0.394	-0.394	-0.393
prior->process[Recruitment].ycs_values{2013}	-0.389	-0.389	-0.393	-0.393	-0.393	-0.389	-0.389	-0.393
prior->process[Recruitment].ycs_values{2014}	-0.396	-0.396	-0.396	-0.396	-0.396	-0.396	-0.396	-0.396
additional_prior->YCS_average_1	0.908	0.908	0.904	0.904	0.904	0.908	0.908	0.904
total_score	2296.970	2296.970	2296.140	2296.140	2296.140	2296.970	2296.970	2296.140

## [1] "CASAL base model convergence information"

## [1] "fmm: have converged: t = 0.00198541 f = 2297.19"                                                        
## [2] "Successful convergence in optimise"                                                                     
## [3] "Minimiser achieved convergence after 53 quasi-Newton iterations using 91 objective function evaluations"

## [1] ""

## [1] "CASAL sensitivity 1 model convergence information"

## [1] "Minimiser convergence threshold: 1e-06"                                                                   
## [2] "fmm: have converged: t = 9.43571e-07 f = 2296.34"                                                         
## [3] "Successful convergence in optimise"                                                                       
## [4] "Minimiser achieved convergence after 197 quasi-Newton iterations using 312 objective function evaluations"

## [1] ""
## [1] "Casal2 betadiff_casal_flags_on model convergence information"
## [1] "fmm: have converged: t = 0.00158129 f = 2296.97"
## [2] "Successful convergence in optimise"             
## [1] ""
## [1] "Casal2 betadiff_casal_flags_off model convergence information"
## [1] "fmm: have converged: t = 0.00158129 f = 2296.97"
## [2] "Successful convergence in optimise"             
## [1] ""
## [1] "Casal2 betadiff_casal_flags_on_low_tol model convergence information"
## [1] "fmm: have converged: t = 4.70876e-07 f = 2296.14"
## [2] "Successful convergence in optimise"              
## [1] ""
## [1] "Casal2 cppad_casal_flags_on model convergence information"
##  [1] "Number of nonzeros in equality constraint Jacobian...:        0"
##  [2] "Number of nonzeros in inequality constraint Jacobian.:       77"
##  [3] "Number of nonzeros in Lagrangian Hessian.............:     3003"
##  [4] "Number of Iterations....: 29"                                   
##  [5] "Number of objective function evaluations             = 52"      
##  [6] "Number of objective gradient evaluations             = 30"      
##  [7] "Number of equality constraint evaluations            = 0"       
##  [8] "Number of inequality constraint evaluations          = 52"      
##  [9] "Number of equality constraint Jacobian evaluations   = 0"       
## [10] "Number of inequality constraint Jacobian evaluations = 30"      
## [11] "Number of Lagrangian Hessian evaluations             = 29"      
## [12] "EXIT: Optimal Solution Found."                                  
## [1] ""
## [1] "Casal2 cppad_casal_flags_off model convergence information"
##  [1] "Number of nonzeros in equality constraint Jacobian...:        0"
##  [2] "Number of nonzeros in inequality constraint Jacobian.:       77"
##  [3] "Number of nonzeros in Lagrangian Hessian.............:     3003"
##  [4] "Number of Iterations....: 29"                                   
##  [5] "Number of objective function evaluations             = 52"      
##  [6] "Number of objective gradient evaluations             = 30"      
##  [7] "Number of equality constraint evaluations            = 0"       
##  [8] "Number of inequality constraint evaluations          = 52"      
##  [9] "Number of equality constraint Jacobian evaluations   = 0"       
## [10] "Number of inequality constraint Jacobian evaluations = 30"      
## [11] "Number of Lagrangian Hessian evaluations             = 29"      
## [12] "EXIT: Optimal Solution Found."                                  
## [1] ""
## [1] "Casal2 adolc_casal_flags_on model convergence information"
## character(0)
## [1] ""
## [1] "Casal2 adolc_casal_flags_off model convergence information"
## character(0)
## [1] ""
## [1] "Casal2 adolc_casal_flags_on_low_tol model convergence information"
## character(0)

## [1] "CASAL base model warnings"

## NULL

## [1] ""

## [1] "CASAL sensitivity 1 model warnings"

##                        parameter estimate lower.bound upper.bound
## 1 selectivity[trawl_sel].male[3]      200           1         200

## [1] ""
## [1] "Casal2 betadiff_casal_flags_on model warnings"
## NULL
## [1] ""
## [1] "Casal2 betadiff_casal_flags_off model warnings"
## NULL
## [1] ""
## [1] "Casal2 betadiff_casal_flags_on_low_tol model warnings"
## $warnings_found
## [1] 1
## 
## $warning_0
## [1] "estimated parameter 'selectivity[trwlFSel_m].sigma_r' was within 0.001 of upper bound 200"
## 
## $type
## [1] "warnings"
## 
## [1] ""
## [1] "Casal2 cppad_casal_flags_on model warnings"
## $warnings_found
## [1] 1
## 
## $warning_0
## [1] "estimated parameter 'selectivity[trwlFSel_m].sigma_r' was within 0.001 of upper bound 200"
## 
## $type
## [1] "warnings"
## 
## [1] ""
## [1] "Casal2 cppad_casal_flags_off model warnings"
## $warnings_found
## [1] 1
## 
## $warning_0
## [1] "estimated parameter 'selectivity[trwlFSel_m].sigma_r' was within 0.001 of upper bound 200"
## 
## $type
## [1] "warnings"
## 
## [1] ""
## [1] "Casal2 adolc_casal_flags_on model warnings"
## NULL
## [1] ""
## [1] "Casal2 adolc_casal_flags_off model warnings"
## NULL
## [1] ""
## [1] "Casal2 adolc_casal_flags_on_low_tol model warnings"
## $warnings_found
## [1] 1
## 
## $warning_0
## [1] "estimated parameter 'selectivity[trwlFSel_m].sigma_r' was within 0.001 of upper bound 200"
## 
## $type
## [1] "warnings"

1.5 Matching of outputs

Time series comparisons with CASAL base model results

## [1] "Catch time series base model comparison for run betadiff_casal_flags_on"
## [1] "Actual catches for trawl match: yes"
## [1] "Actual catches for line_home match: yes"
## [1] "Actual catches for line_spawn match: yes"
## [1] ""
## [1] "Catch time series base model comparison for run betadiff_casal_flags_off"
## [1] "Actual catches for trawl match: yes"
## [1] "Actual catches for line_home match: yes"
## [1] "Actual catches for line_spawn match: yes"
## [1] ""
## [1] "Catch time series base model comparison for run betadiff_casal_flags_on_low_tol"
## [1] "Actual catches for trawl match: yes"
## [1] "Actual catches for line_home match: yes"
## [1] "Actual catches for line_spawn match: yes"
## [1] ""
## [1] "Catch time series base model comparison for run cppad_casal_flags_on"
## [1] "Actual catches for trawl match: yes"
## [1] "Actual catches for line_home match: yes"
## [1] "Actual catches for line_spawn match: yes"
## [1] ""
## [1] "Catch time series base model comparison for run cppad_casal_flags_off"
## [1] "Actual catches for trawl match: yes"
## [1] "Actual catches for line_home match: yes"
## [1] "Actual catches for line_spawn match: yes"
## [1] ""
## [1] "Catch time series base model comparison for run adolc_casal_flags_on"
## [1] "Actual catches for trawl match: yes"
## [1] "Actual catches for line_home match: yes"
## [1] "Actual catches for line_spawn match: yes"
## [1] ""
## [1] "Catch time series base model comparison for run adolc_casal_flags_off"
## [1] "Actual catches for trawl match: yes"
## [1] "Actual catches for line_home match: yes"
## [1] "Actual catches for line_spawn match: yes"
## [1] ""
## [1] "Catch time series base model comparison for run adolc_casal_flags_on_low_tol"
## [1] "Actual catches for trawl match: yes"
## [1] "Actual catches for line_home match: yes"
## [1] "Actual catches for line_spawn match: yes"
## [1] ""

Derived quantities

SB0, SBcurrent, MSY, F_MSY, others…

1.6 Plots

Comparison plots

## [1] "CASAL base parameter correlation range (excluding 1.0): -0.735942 0.9329"

## [1] "CASAL sensitivity 1 parameter correlation range (excluding 1.0): -0.986887 0.996747"

## [1] "Casal2 betadiff_casal_flags_on parameter correlation range (excluding 1.0): -0.762745537546469 0.932179473694354"

## [1] "Casal2 betadiff_casal_flags_off parameter correlation range (excluding 1.0): -0.762745537546469 0.932179473694354"

## [1] "Casal2 betadiff_casal_flags_on_low_tol parameter correlation range (excluding 1.0): -0.98942900392945 0.979130660174252"

## [1] "Casal2 cppad_casal_flags_on parameter correlation range (excluding 1.0): -0.98942900392945 0.979130660174252"

## [1] "Casal2 cppad_casal_flags_off parameter correlation range (excluding 1.0): -0.98942900392945 0.979130660174252"

## [1] "Casal2 adolc_casal_flags_on parameter correlation range (excluding 1.0): -0.762745537546469 0.932179473694354"

## [1] "Casal2 adolc_casal_flags_off parameter correlation range (excluding 1.0): -0.762745537546469 0.932179473694354"

## [1] "Casal2 adolc_casal_flags_on_low_tol parameter correlation range (excluding 1.0): -0.98942900392945 0.979130660174252"